Okay, now I understand. About my example below: keep in mind I am simply adapting a different axle to the car I am currently building not starting from scratch, so I had to run a shorter upper link due to the way the car's unibody is built.
The way I did my 3 link: I raised and leveled the car, then set my axle on stands below it with the pinion flange at 90 degrees to the body. The important part: the axle has to be at the correct ride height. I calculated my link lengths from that. I have enough adjustment in the links to change the pinion angle up or down as needed.
Pinion angle change through travel is most affected by whether the links are the same length. If the top link is a lot shorter but the links are parallel as viewed from the side, the pinion will angle downwards as the axle rises. If the lower links are a lot shorter, the reverse will happen. This is also a function of how much travel the axle will have, it's going to be a lot more pronounced on something whith a whole lot of suspension travel (rock crawler etc) than, say, a road race car with a total of 4" of travel.
Since you are starting from scratch, I'd recommend making the links as long as possible and keep them as parallel as possible when viewed from the side. 44's advice about angled links vs Panhard is good, it's a lot easier to do the PH and get things right. His angle recommendations sound good too.